zeq-galaxy-tools 1.287.124

Zeq molecular and scientific connector tools for Galaxy - 12 tools (6 originals + 6 TM siblings): PubChem 3D, RCSB PDB, AlphaFold, ChEMBL, MD Simulator, NIST Spectral - powered by 1.287 Hz HulyaPulse

Zeq OS Galaxy Tools

Twelve production-ready molecular & scientific connector tools for Galaxy — 6 originals + 6 time-modulation siblings. Powered by the Zeq API with 1.287 Hz HulyaPulse synchronization and CKO envelope verification.

Quick Start

pip install zeq-galaxy-tools

Get your Zeq API key at https://www.zeq.dev/dashboard

Tools

Original Tools (6)

Tool	Description	Data Source
zeq-pubchem-3d	3D molecular structures, bond lengths, properties	PubChem
zeq-rcsb-pdb	Experimental protein structures (X-ray, cryo-EM)	RCSB PDB
zeq-alphafold	AI-predicted protein structures with confidence	AlphaFold DB
zeq-chembl	Bioactivity data, IC50/EC50, pharmacology	ChEMBL
zeq-md-simulator	Molecular dynamics (Lennard-Jones, Morse, Coulomb)	Simulation engine
zeq-nist-spectral	Spectral emission lines for 16 elements	NIST ASD

Time-Modulation Siblings (6)

Each original tool has a TM (time-modulation) sibling that applies 1.287 Hz HulyaPulse temporal filtering:

Tool	Description
zeq-pubchem-3d-tm	Time-modulated PubChem 3D structures
zeq-rcsb-pdb-tm	Time-modulated RCSB PDB structures
zeq-alphafold-tm	Time-modulated AlphaFold predictions
zeq-chembl-tm	Time-modulated ChEMBL bioactivity data
zeq-md-simulator-tm	Time-modulated molecular dynamics
zeq-nist-spectral-tm	Time-modulated spectral analysis

Usage

Command Line

# Fetch aspirin 3D structure
zeq-pubchem-3d --zeq_api_key YOUR_KEY --molecule aspirin --mode all \
  --output_atoms atoms.tsv --output_bonds bonds.tsv \
  --output_properties props.tsv --output_json summary.json

# Fetch hemoglobin from PDB
zeq-rcsb-pdb --zeq_api_key YOUR_KEY --pdb_id 4HHB --mode all \
  --output_atoms atoms.tsv --output_summary summary.tsv --output_json data.json

# AlphaFold predicted structure
zeq-alphafold --zeq_api_key YOUR_KEY --uniprot_id P69905 --mode all \
  --output_atoms atoms.tsv --output_confidence conf.tsv --output_json summary.json

# ChEMBL bioactivity data
zeq-chembl --zeq_api_key YOUR_KEY --molecule ibuprofen --mode all \
  --output_activities activities.tsv --output_molecule mol.tsv --output_json data.json

# Run molecular dynamics
zeq-md-simulator --zeq_api_key YOUR_KEY --potential lennard_jones \
  --num_particles 50 --num_steps 1000 \
  --output_trajectory traj.tsv --output_energy energy.tsv --output_json summary.json

# Analyze iron emission spectrum
zeq-nist-spectral --zeq_api_key YOUR_KEY --element Fe --mode all \
  --output_lines lines.tsv --output_spectrum spectrum.tsv --output_json summary.json

Python API

from zeq_galaxy_tools.tools import zeq_pubchem_3d
import subprocess, sys

# Or call directly
subprocess.run([sys.executable, "-m", "zeq_galaxy_tools.tools.zeq_pubchem_3d",
    "--zeq_api_key", "YOUR_KEY", "--molecule", "caffeine", "--mode", "all",
    "--output_atoms", "atoms.tsv", "--output_bonds", "bonds.tsv",
    "--output_properties", "props.tsv", "--output_json", "summary.json"])

Galaxy ToolShed

All tools are also available on the Galaxy ToolShed for use within Galaxy workflows.

Docker

docker pull azeq13/zeq-galaxy-tools:1.287.124
docker run azeq13/zeq-galaxy-tools:1.287.124 zeq-pubchem-3d \
  --zeq_api_key YOUR_KEY --molecule aspirin --mode all \
  --output_atoms /data/atoms.tsv --output_bonds /data/bonds.tsv \
  --output_properties /data/props.tsv --output_json /data/summary.json

HulyaPulse Modulation

Original tools support optional --hulyapulse flag. Time-modulation siblings apply 1.287 Hz temporal filtering by default. Both provide:

• Phase-locked synchronization with Zeq OS infrastructure
• Graceful API rate limiting
• Verified CKO envelope generation with zeqProof
• Zeqond period alignment (0.777 s)

Zeq OS Integration

• Version: 1.287.124
• HulyaPulse frequency: 1.287 Hz
• Zeqond period: 0.777 s
• KO42 Metric Tensioner: Prime Directive
• API: https://www.zeq.dev
• SDK: https://sdk.1.287hz.com/

Requirements

• Python 3.8+
• Zeq API key (get yours at https://www.zeq.dev/dashboard)
• No external dependencies (Python standard library only)

Citations

• Zeq OS Paper: https://doi.org/10.5281/zenodo.18158152
• Zeq OS Framework: https://doi.org/10.5281/zenodo.15825138
• AlphaFold2: Jumper et al. (2021). Nature. https://doi.org/10.1038/s41586-021-03819-2

License

1.287 HULYAS ZEQ Public License (1.287HZ) - Zeq. H, Zeq OS 1.287 Hz Limited

Links

• Zeq OS: https://hulyas.org
• Zeq API: https://www.zeq.dev
• Galaxy ToolShed: https://toolshed.g2.bx.psu.edu/view/Zeq
• SDK: https://sdk.1.287hz.com/